Chimeric Detective Report

28

Contigs Analyzed

7

Contigs Split

2

Contigs Preserved

0.66

Mean Confidence

📊 Summary Visualizations

Chimera Type Distribution

Confidence Score Distributions

Decision Summary

Evidence Types Overview

🔍 Detailed Analysis Results

Contig ID	Chimera Type	Confidence	Decision	Breakpoint	Evidence Types	Explanation
contig_003	technical_artifact	0.8	SPLIT	3122	gc_content_shift, kmer_composition_change	Contig contig_003 shows clear evidence of being a technical chimera resulting from misassembly. At position 3,122, there is a 1.1x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.33) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.77.
contig_013	technical_artifact	0.5	PRESERVE	2922	gc_content_shift, kmer_composition_change	Contig contig_013 shows clear evidence of being a technical chimera resulting from misassembly. At position 2,922, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.27) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.76.
chimeric_001	technical_artifact	0.7	SPLIT	1356	gc_content_shift, kmer_composition_change	Contig chimeric_001 shows clear evidence of being a technical chimera resulting from misassembly. At position 1,356, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.30) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.78.
chimeric_004	technical_artifact	0.7	SPLIT	1488	gc_content_shift, kmer_composition_change	Contig chimeric_004 shows clear evidence of being a technical chimera resulting from misassembly. At position 1,488, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.32) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.78.
cov_chimeric_003	technical_artifact	0.5	PRESERVE	926	gc_content_shift, kmer_composition_change	Contig cov_chimeric_003 shows clear evidence of being a technical chimera resulting from misassembly. At position 926, there is a 1.1x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.26) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.76.
contig_009	technical_artifact	0.5	SPLIT	4890	gc_content_shift, kmer_composition_change	Contig contig_009 shows clear evidence of being a technical chimera resulting from misassembly. At position 4,890, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.33) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.75.
contig_018	technical_artifact	0.7	SPLIT	1585	gc_content_shift, kmer_composition_change	Contig contig_018 shows clear evidence of being a technical chimera resulting from misassembly. At position 1,585, there is a 1.1x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.34) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.76.
contig_005	technical_artifact	0.8	SPLIT	6302	gc_content_shift, kmer_composition_change	Contig contig_005 shows clear evidence of being a technical chimera resulting from misassembly. At position 6,302, there is a 1.2x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.27) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.76.
contig_013	technical_artifact	1.0	PRESERVE	380	gc_content_shift, kmer_composition_change	Contig contig_013 shows clear evidence of being a technical chimera resulting from misassembly. At position 380, there is a 1.1x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.23) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.77.
contig_005	technical_artifact	0.5	SPLIT	4175	gc_content_shift, kmer_composition_change	Contig contig_005 shows clear evidence of being a technical chimera resulting from misassembly. At position 4,175, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.16) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.77.
contig_003	technical_artifact	0.5	SPLIT	5713	gc_content_shift, kmer_composition_change	Contig contig_003 shows clear evidence of being a technical chimera resulting from misassembly. At position 5,713, there is a 1.1x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.13) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.76.
contig_005	technical_artifact	0.5	SPLIT	3474	gc_content_shift, kmer_composition_change	Contig contig_005 shows clear evidence of being a technical chimera resulting from misassembly. At position 3,474, there is a 1.0x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.20) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.78.
contig_006	technical_artifact	0.8	SPLIT	2229	gc_content_shift, kmer_composition_change	Contig contig_006 shows clear evidence of being a technical chimera resulting from misassembly. At position 2,229, there is a 1.1x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.21) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.77.
contig_009	technical_artifact	0.8	SPLIT	6261	gc_content_shift, kmer_composition_change	Contig contig_009 shows clear evidence of being a technical chimera resulting from misassembly. At position 6,261, there is a 1.3x change in read coverage and a significant shift in sequence composition. The low number of paired reads spanning this junction (spanning ratio: 0.26) further supports this being an assembly artifact rather than biological recombination. Confidence: 0.75.

📈 Individual Contig Details

Click on the links below to view detailed analysis for each chimeric contig:

ℹ️ Methodology & Interpretation

Detection Methods

Chimeric contigs are detected using multiple complementary approaches:

Coverage Discontinuities: Sharp changes in read coverage depth
Sequence Composition: Changes in GC content and k-mer frequencies
Taxonomic Classification: Transitions between different viral/host lineages
Read Pair Orientation: Inconsistent paired-end read orientations

Classification Categories

Technical Artifacts: Assembly errors, typically split
PCR Chimeras: Amplification artifacts, typically split
Biological Recombination: Genuine recombination events, preserved
Provirus Integration: Virus-host integration sites, flagged

Confidence Scores

Confidence scores range from 0-1, with higher scores indicating stronger evidence for the classification. Scores above 0.8 are considered high confidence, 0.5-0.8 medium confidence, and below 0.5 low confidence.